In this study, the removal of Escherichia coli (E. coli) and MS-2 bacteriophage with silica powder and crystalline sand particles with NH2-functionalised self-assembled monolayers (SAMs) was investigated. This study demonstrated that the removal of E. coli and MS-2 bacteriophage in the company of SAM coated substrates increased substantially over the maximum period, where the highest concentration of SAM covered silica powder achieved the fastest removal of both microorganisms, reaching the detection limit of the assay at 20 minutes. Removal was minimal with SAM coated quartz and no removal observed for unmodified quartz sand. SEM (scanning electron micrograph) pictures clearly show E. coli on SAM surfaces. With a greater removal observed for larger SAM concentrations, it may be suggested that the higher the concentration of the SAM, the faster the removal of the microorganisms. The removal is believed to be due to electrostatic attraction of the microorganisms to the positively charged surface of the functionalised particles.